The genome sequence of the Lobe-spurred Furrow Bee, Lasioglossum pauxillum (Schenck, 1853)

We present a genome assembly from an individual female Lasioglossum pauxillum (the Lobe-spurred Furrow Bee; Arthropoda; Insecta; Hymenoptera; Halictidae). The genome sequence is 432.0 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 27.71 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,353 protein coding genes.

The snailplot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3.The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla.Most (99.57%) of the assembly sequence was assigned to 9 chromosomal-level scaffolds, representing 9 autosomes.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.

Background
The Lobe-spurred Furrow Bee, Lasioglossum pauxillum, is a small (forewing length 3.5-4.5 mm) dark bee in the family Halictidae.It occurs throughout Europe, from Portugal to Georgia, and into north Africa.In the UK is it common and widespread across southern England and occurs into the Midlands and Wales.The inner spur of the hind tibia of females has broadly rounded projections rather than narrow and pointed teeth, which is unique amongst British Lasioglossum species.Females also have a carinate propodeum, pale wing stigmas, a complete ridge defining the apical depression of tergite one.and the antennal flagella is usually orange underneath.
L. pauxillum is associated with open habitats, especially chalk grassland where it can be abundant.It is a primitively eusocial species (Plateaux-Quénu, 2008), with overwintered females emerging from April and producing workers by early summer.Males and gynes are produced from July to October, with mated females overwintering.Nest often have a 'turret-like' entrance (Westrich, 1989) and occur in bare or sparsely vegetated, level soil, in aggregations that can reach large numbers (Pesenko et al., 2000).Macrocyclic lactones are used as queen recognition signals, regulating worker behaviour and physiology, and therefore maintaining reproductive harmony (Steitz et al., 2019).A wide range of flowers are visited for nectar, including umbellifers, composites, buttercups, spring-flowering shrubs and especially common fleabane, Pulicaria dysenterica (Falk & Lewington, 2019).It is oligolectic, visiting fewer species of flowers for pollen than other Lasioglossum species (Polidori et al., 2010), but from a taxonomically broad range (Beil et al., 2008).
The complete genome sequence for this species will facilitate studies into the evolution of sociality, reproductive systems and Hymenopteran taxonomy.

Genome sequence report
The genome was sequenced from one female Lasioglossum pauxillum (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.78,.A total of 59-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 40 missing joins or mis-joins, reducing the scaffold number by 52.05%, and increasing the scaffold N50 by 100.79%. The final assembly has a total length of 432.0 Mb in 35 sequence scaffolds with a scaffold N50 of 48.2 Mb (Table 1).

Sequencing
Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers' instructions.DNA sequencing was performed by the Scientific Operations core at the WSI on a Pacific Biosciences SEQUEL II instrument.Hi-C data were also generated from remaining tissue of iyLasPaux1 using the Arima2 kit and sequenced on the HiSeq X Ten instrument.

Genome assembly, curation and evaluation
Assembly was carried out with Hifiasm (Cheng et al., 2021) and haplotypic duplication was identified and removed with purge_dups (Guan et al., 2020).The assembly was then scaffolded with Hi-C data (Rao et al., 2014) using YaHS (Zhou et al., 2023).The assembly was checked for contamination    (Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
Table 3 contains a list of relevant software tool versions and sources.

Genome annotation
The Ensembl gene annotation system (Aken et al., 2016) was used to generate annotation for the Lasioglossum pauxillum assembly (GCA_933228785.1).Annotation was created primarily through alignment of transcriptomic data to the genome, with gap filling via protein-to-genome alignments and corrected using the gEVAL system (Chow et al., 2016) as described previously (Howe et al., 2021).Manual curation was performed using gEVAL, HiGlass (Kerpedjiev et al., 2018) and Pretext (Harry, 2022).The mitochondrial of a select set of proteins from UniProt (UniProt Consortium, 2019).

Wellcome Sanger Institute -Legal and Governance
The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner.The submission of materials by a Darwin Tree of Life Partner is subject to the 'Darwin Tree of Life Project Sampling Code of Practice', which can be found in full on the Darwin Tree of Life website here.By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project.
Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use.The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible.The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material

Daniel Garcia-Souto
University of Santiago de Compostela, Galicia, Spain The manuscript presents a high-quality genome assembly of a female of Lasioglossum pauxillum, utilizing cutting-edge sequencing techniques and thorough validation methods.The assembly achieved 59-fold coverage with Pacific Biosciences HiFi long reads and was scaffolded with Hi-C data, resulting in 35 sequence scaffolds with an N50 of 48.2 Mb.This represents a significant improvement over the previous genome assembly for this species (GCA_028455745), which was not referenced in the manuscript (and likely should have).Although initially, the scaffold count exceeded the species' known diploid number (2n=18), a subsequent manual curation reduced the scaffold numbers by 52.05% and doubled the scaffold N50, achieving a complete chromosomelevel assembly.Thus, the final assembly is nearly complete, with 99.57% of the sequence assigned to nine chromosomal scaffolds and a BUSCO completeness score of 95.7%.This work represents a valuable genomic resource for the entomology community.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Molecular cytogenetics, Genome assembly, Gene Annotation, Repetitive DNA

Introduction:
The authors have provided a strong overview of the species' ecology.However, the transition to the potential uses of the genome feels abrupt.A smoother transition from the species' biology to the relevance of its genome would improve readability.For instance, introducing the topic of sociality before discussing the genome's role in studying the evolution of sociality would be beneficial.

Genome Sequence Report:
The genome quality appears to be very high-well done!Methods: Could the authors specify how RNA was extracted and from which tissues?
The chromosome count in Lasioglossum pauxillum seems lower compared to other Lasioglossum species, such as Lasioglossum lativentre, which has 14 chromosomes.I recommend the authors double-check their manual curation of the chromosome count.

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Genomics I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.The author presents a high quality genome sequence of Lasioglossum pauxillum (Schenck, 1853).
The author provides all the sufficient information of the materials, sequencing details, and bioinformatics tools used to achieve a highly contiguous genome of L. pauxillum.I am quite intrigued by the size of the genome of the L. pauxillum.While not required, I am curious to learn how the size of this bee's genome compares to other bee genome sequences.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.

Figure 2 .
Figure 2. Genome assembly of Lasioglossum pauxillum, iyLasPaux1.1:metrics.The BlobToolKit Snailplot shows N50 metrics and BUSCO gene completeness.The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 432,014,419 bp assembly.The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (55,061,150 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (48,162,910 and 42,843,013 bp), respectively.The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude.The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot.A summary of complete, fragmented, duplicated and missing BUSCO genes in the hymenoptera_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAKOFU01/dataset/CAKOFU01/snail.

Figure 3 .
Figure 3. Genome assembly of Lasioglossum pauxillum, iyLasPaux1.1:BlobToolKit GC-coverage plot.Scaffolds are coloured by phylum.Circles are sized in proportion to scaffold length.Histograms show the distribution of scaffold length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAKOFU01/dataset/CAKOFU01/blob.

Figure 4 .
Figure 4. Genome assembly of Lasioglossum pauxillum, iyLasPaux1.1:BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all scaffolds.Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAKOFU01/dataset/CAKOFU01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Lasioglossum pauxillum, iyLasPaux1.1:Hi-C contact map of the iyLasPaux1.1 assembly, visualised using HiGlass.Chromosomes are shown in order of size from left to right and top to bottom.An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=WN94LQFxSki1yrVGwhd-EA.

Figure 1 :
Figure 1: While a fluidX tube is used as a scale, this may not be familiar to all readers.I suggest adding a scale reference based on the tube's dimensions.

Reviewer
Report 01 August 2024 https://doi.org/10.21956/wellcomeopenres.23177.r87631© 2024 Uhuad Koch J.This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Jonathan Berenguer Uhuad Koch USDA-ARS Pollinating Insect Research Unit, Logan, Utah, USA

Table 1 . Genome data for Lasioglossum pauxillum, iyLasPaux1.1. Project accession data
(Jay et al., 2023))enchmarks are adapted from column VGP-2020 of "Table1: Proposed standards and metrics for defining genome assembly quality" from(Rhie et al., 2021).**BUSCOscoresbased on the hymenoptera_odb10 BUSCO set using version 5.3.2.C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison.A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/CAKOFU01/dataset/CAKOFU01/busco.51.78, longitude -1.32) on 2019-07-18 by potting.The specimen was collected and identified by Liam Crowley (University of Oxford) and preserved on dry ice.The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up.In sample preparation, the iyLasPaux1 sample was weighed and dissected on dry ice(Jay et al., 2023).Tissue from the whole organism was homogenised using a PowerMasher II tissue disruptor(Denton et al., 2023a).HMW DNA was extracted

Open Peer Review Current Peer Review Status: Version 1
This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.